Depends on which sport or sports you are asking about.
UCLA they have 101 national championships in all sports. (11 in basketball)
UCLA with 100
Stanford, with 99 total national championships. UCLA is first with 106, and USC is third with 91.
In college football Alabama has the most national championships with 13 while Notre Dame comes in second with 12. In College Hockey Bemidji State University has 13 national championships